Multiple sequence alignment - TraesCS2B01G117100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2B01G117100 chr2B 100.000 4256 0 0 1 4256 80199563 80203818 0.000000e+00 7860.0
1 TraesCS2B01G117100 chr2B 86.054 2352 309 13 876 3214 79709220 79706875 0.000000e+00 2508.0
2 TraesCS2B01G117100 chr2B 83.764 2285 343 19 876 3142 79671883 79669609 0.000000e+00 2139.0
3 TraesCS2B01G117100 chr2B 95.652 69 3 0 812 880 80200438 80200506 1.250000e-20 111.0
4 TraesCS2B01G117100 chr2D 95.749 3223 103 17 508 3712 51252784 51255990 0.000000e+00 5162.0
5 TraesCS2B01G117100 chr2D 86.522 2352 289 16 876 3214 51160287 51157951 0.000000e+00 2562.0
6 TraesCS2B01G117100 chr2D 90.466 472 28 5 3775 4233 51255987 51256454 1.310000e-169 606.0
7 TraesCS2B01G117100 chr2D 86.974 499 24 10 18 493 51252322 51252802 1.360000e-144 523.0
8 TraesCS2B01G117100 chr2D 94.203 69 4 0 812 880 51253154 51253222 5.820000e-19 106.0
9 TraesCS2B01G117100 chr2A 94.722 3221 112 23 511 3712 52756180 52759361 0.000000e+00 4953.0
10 TraesCS2B01G117100 chr2A 86.619 2354 292 18 876 3214 52573270 52570925 0.000000e+00 2580.0
11 TraesCS2B01G117100 chr2A 84.011 2089 312 16 1066 3142 52427833 52425755 0.000000e+00 1988.0
12 TraesCS2B01G117100 chr2A 81.640 1732 284 23 877 2592 52540943 52539230 0.000000e+00 1406.0
13 TraesCS2B01G117100 chr2A 90.870 471 22 7 3775 4233 52759358 52759819 2.810000e-171 612.0
14 TraesCS2B01G117100 chr2A 86.890 328 23 5 18 343 52749441 52749750 2.440000e-92 350.0
15 TraesCS2B01G117100 chr2A 83.333 210 27 5 677 883 52541075 52540871 2.020000e-43 187.0
16 TraesCS2B01G117100 chr2A 80.000 245 33 8 3409 3647 52570669 52570435 2.630000e-37 167.0
17 TraesCS2B01G117100 chr2A 95.652 92 3 1 389 479 52756011 52756102 3.430000e-31 147.0
18 TraesCS2B01G117100 chr2A 92.857 70 4 1 812 880 52756522 52756591 2.710000e-17 100.0
19 TraesCS2B01G117100 chr2A 92.727 55 3 1 329 382 52755929 52755983 1.270000e-10 78.7
20 TraesCS2B01G117100 chr7D 82.270 2397 401 19 876 3263 76396820 76399201 0.000000e+00 2050.0
21 TraesCS2B01G117100 chr7A 81.917 2400 405 23 876 3263 80313783 80316165 0.000000e+00 2001.0
22 TraesCS2B01G117100 chr7A 82.194 2078 350 12 1190 3263 82155452 82153391 0.000000e+00 1770.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G117100 chr2B 80199563 80203818 4255 False 3985.50 7860 97.8260 1 4256 2 chr2B.!!$F1 4255
1 TraesCS2B01G117100 chr2B 79706875 79709220 2345 True 2508.00 2508 86.0540 876 3214 1 chr2B.!!$R2 2338
2 TraesCS2B01G117100 chr2B 79669609 79671883 2274 True 2139.00 2139 83.7640 876 3142 1 chr2B.!!$R1 2266
3 TraesCS2B01G117100 chr2D 51157951 51160287 2336 True 2562.00 2562 86.5220 876 3214 1 chr2D.!!$R1 2338
4 TraesCS2B01G117100 chr2D 51252322 51256454 4132 False 1599.25 5162 91.8480 18 4233 4 chr2D.!!$F1 4215
5 TraesCS2B01G117100 chr2A 52425755 52427833 2078 True 1988.00 1988 84.0110 1066 3142 1 chr2A.!!$R1 2076
6 TraesCS2B01G117100 chr2A 52570435 52573270 2835 True 1373.50 2580 83.3095 876 3647 2 chr2A.!!$R3 2771
7 TraesCS2B01G117100 chr2A 52755929 52759819 3890 False 1178.14 4953 93.3656 329 4233 5 chr2A.!!$F2 3904
8 TraesCS2B01G117100 chr2A 52539230 52541075 1845 True 796.50 1406 82.4865 677 2592 2 chr2A.!!$R2 1915
9 TraesCS2B01G117100 chr7D 76396820 76399201 2381 False 2050.00 2050 82.2700 876 3263 1 chr7D.!!$F1 2387
10 TraesCS2B01G117100 chr7A 80313783 80316165 2382 False 2001.00 2001 81.9170 876 3263 1 chr7A.!!$F1 2387
11 TraesCS2B01G117100 chr7A 82153391 82155452 2061 True 1770.00 1770 82.1940 1190 3263 1 chr7A.!!$R1 2073

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
132 133 0.038618 CCAAAGCAAAAGGTACGGCC 60.039 55.0 0.00 0.0 37.58 6.13 F
213 214 0.391597 TGGTTCAGTCCGTGTTCTCC 59.608 55.0 0.00 0.0 0.00 3.71 F
1484 1568 0.454600 GACACCGGTCTCTATGCGAA 59.545 55.0 2.59 0.0 40.99 4.70 F
2850 2949 1.043816 GCTACATCTGCTGGCTCCTA 58.956 55.0 0.00 0.0 0.00 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1484 1568 0.250338 GTCGTCAAAGGAAGGGTGCT 60.250 55.0 0.00 0.00 0.00 4.40 R
1739 1827 0.307760 GGCGCATACCTTGTACATGC 59.692 55.0 10.83 8.09 41.29 4.06 R
3207 3306 0.397941 CTCTTGGGGAGACAGCAACA 59.602 55.0 0.00 0.00 44.45 3.33 R
4138 4337 0.770499 TTTCCCATGTGACAGGAGCA 59.230 50.0 0.00 0.00 0.00 4.26 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 4.151582 CGGTATTGGCGACGGGGT 62.152 66.667 0.00 0.00 0.00 4.95
99 100 0.258774 GTGCCATGTCCCATACCCTT 59.741 55.000 0.00 0.00 0.00 3.95
100 101 0.258484 TGCCATGTCCCATACCCTTG 59.742 55.000 0.00 0.00 0.00 3.61
129 130 0.589223 TCGCCAAAGCAAAAGGTACG 59.411 50.000 0.00 0.00 39.83 3.67
132 133 0.038618 CCAAAGCAAAAGGTACGGCC 60.039 55.000 0.00 0.00 37.58 6.13
141 142 3.395630 GGTACGGCCTTCTTCCCA 58.604 61.111 0.00 0.00 0.00 4.37
142 143 1.681076 GGTACGGCCTTCTTCCCAA 59.319 57.895 0.00 0.00 0.00 4.12
159 160 1.452108 AAGCACTAGGAATGGCCGC 60.452 57.895 0.00 0.00 43.43 6.53
200 201 2.231478 GAGGTCGTCTCATCTTGGTTCA 59.769 50.000 4.21 0.00 42.02 3.18
201 202 2.232452 AGGTCGTCTCATCTTGGTTCAG 59.768 50.000 0.00 0.00 0.00 3.02
202 203 2.028930 GGTCGTCTCATCTTGGTTCAGT 60.029 50.000 0.00 0.00 0.00 3.41
203 204 3.246619 GTCGTCTCATCTTGGTTCAGTC 58.753 50.000 0.00 0.00 0.00 3.51
204 205 2.231478 TCGTCTCATCTTGGTTCAGTCC 59.769 50.000 0.00 0.00 0.00 3.85
205 206 2.611518 GTCTCATCTTGGTTCAGTCCG 58.388 52.381 0.00 0.00 0.00 4.79
206 207 2.028930 GTCTCATCTTGGTTCAGTCCGT 60.029 50.000 0.00 0.00 0.00 4.69
207 208 2.029020 TCTCATCTTGGTTCAGTCCGTG 60.029 50.000 0.00 0.00 0.00 4.94
208 209 1.691976 TCATCTTGGTTCAGTCCGTGT 59.308 47.619 0.00 0.00 0.00 4.49
209 210 2.104111 TCATCTTGGTTCAGTCCGTGTT 59.896 45.455 0.00 0.00 0.00 3.32
210 211 2.234300 TCTTGGTTCAGTCCGTGTTC 57.766 50.000 0.00 0.00 0.00 3.18
211 212 1.760613 TCTTGGTTCAGTCCGTGTTCT 59.239 47.619 0.00 0.00 0.00 3.01
212 213 2.135933 CTTGGTTCAGTCCGTGTTCTC 58.864 52.381 0.00 0.00 0.00 2.87
213 214 0.391597 TGGTTCAGTCCGTGTTCTCC 59.608 55.000 0.00 0.00 0.00 3.71
214 215 0.666577 GGTTCAGTCCGTGTTCTCCG 60.667 60.000 0.00 0.00 0.00 4.63
215 216 1.006571 TTCAGTCCGTGTTCTCCGC 60.007 57.895 0.00 0.00 0.00 5.54
249 250 3.876914 TGTGTTTCTGCCTGTTTGTAGAG 59.123 43.478 0.00 0.00 0.00 2.43
265 266 8.414003 TGTTTGTAGAGTATAATCTGATTCGCT 58.586 33.333 12.86 3.85 0.00 4.93
278 279 0.610174 ATTCGCTGAGCACCAGAAGA 59.390 50.000 4.88 5.73 45.78 2.87
301 302 3.365265 CCACTGGAACGCCAAGGC 61.365 66.667 0.00 0.00 45.41 4.35
307 308 3.423154 GAACGCCAAGGCCAGACG 61.423 66.667 5.01 3.52 37.98 4.18
324 325 2.390599 CGTTCCATGCACCCACTCG 61.391 63.158 0.00 0.00 0.00 4.18
363 365 2.479566 TTTCTTAGTGCAGCTCCTGG 57.520 50.000 0.00 0.00 31.21 4.45
376 378 4.558697 GCAGCTCCTGGTAATTTTCGTTTT 60.559 41.667 0.00 0.00 31.21 2.43
382 384 9.628746 GCTCCTGGTAATTTTCGTTTTAAAATA 57.371 29.630 3.52 0.00 37.93 1.40
479 503 6.820335 TGTCCAAGGATCTGTTGACATATAG 58.180 40.000 9.22 0.00 0.00 1.31
480 504 5.698545 GTCCAAGGATCTGTTGACATATAGC 59.301 44.000 9.22 0.00 0.00 2.97
481 505 5.366477 TCCAAGGATCTGTTGACATATAGCA 59.634 40.000 9.22 0.00 0.00 3.49
483 507 4.876125 AGGATCTGTTGACATATAGCACG 58.124 43.478 0.00 0.00 0.00 5.34
485 509 5.535030 AGGATCTGTTGACATATAGCACGTA 59.465 40.000 0.00 0.00 0.00 3.57
486 510 5.629849 GGATCTGTTGACATATAGCACGTAC 59.370 44.000 0.00 0.00 0.00 3.67
487 511 5.830000 TCTGTTGACATATAGCACGTACT 57.170 39.130 0.00 0.00 0.00 2.73
488 512 5.817988 TCTGTTGACATATAGCACGTACTC 58.182 41.667 0.00 0.00 0.00 2.59
489 513 5.589050 TCTGTTGACATATAGCACGTACTCT 59.411 40.000 0.00 0.00 0.00 3.24
490 514 6.095021 TCTGTTGACATATAGCACGTACTCTT 59.905 38.462 0.00 0.00 0.00 2.85
491 515 6.627243 TGTTGACATATAGCACGTACTCTTT 58.373 36.000 0.00 0.00 0.00 2.52
492 516 7.094631 TGTTGACATATAGCACGTACTCTTTT 58.905 34.615 0.00 0.00 0.00 2.27
493 517 7.601130 TGTTGACATATAGCACGTACTCTTTTT 59.399 33.333 0.00 0.00 0.00 1.94
818 890 8.013947 CGCTGGATTTATCAACTGATGATTAAG 58.986 37.037 5.72 0.00 46.85 1.85
937 1012 4.952460 TCGTGCTGTATAAAGATTACCCC 58.048 43.478 0.00 0.00 0.00 4.95
1068 1152 2.600731 CTCTTTCCTACACTCGCACTG 58.399 52.381 0.00 0.00 0.00 3.66
1128 1212 1.203287 GCCACAAAATCCTCTGCTTCC 59.797 52.381 0.00 0.00 0.00 3.46
1484 1568 0.454600 GACACCGGTCTCTATGCGAA 59.545 55.000 2.59 0.00 40.99 4.70
1739 1827 4.147449 TCCTGGCGCTCACATCGG 62.147 66.667 7.64 1.50 0.00 4.18
1954 2049 2.792947 GGCAATAGCGGTCCGAGGA 61.793 63.158 17.49 0.00 43.41 3.71
2028 2123 1.451028 GGATCGGAGCTTTGCTGCT 60.451 57.895 9.20 0.00 44.73 4.24
2051 2146 2.060004 CTGCATCTCGGCAATGGCAG 62.060 60.000 7.75 3.90 44.40 4.85
2303 2401 1.560505 GCCACCATGGTTCAGGATTT 58.439 50.000 21.13 0.00 40.46 2.17
2523 2622 1.816961 GCACCAGGCCTCAATATCCTG 60.817 57.143 0.00 0.00 45.24 3.86
2850 2949 1.043816 GCTACATCTGCTGGCTCCTA 58.956 55.000 0.00 0.00 0.00 2.94
2979 3078 1.203758 ACATCGACGCCATTCACAGTA 59.796 47.619 0.00 0.00 0.00 2.74
3024 3123 1.872952 CCAGCAAACTCGACATTCACA 59.127 47.619 0.00 0.00 0.00 3.58
3240 3339 0.461548 CAAGAGGCGATACTGCTCCA 59.538 55.000 0.00 0.00 34.52 3.86
3358 3513 7.961325 ACTGGTGCAAAATTTTAGGTTAATG 57.039 32.000 2.44 0.00 0.00 1.90
3360 3515 5.406780 TGGTGCAAAATTTTAGGTTAATGCG 59.593 36.000 2.44 0.00 35.40 4.73
3362 3517 6.400621 GGTGCAAAATTTTAGGTTAATGCGTC 60.401 38.462 2.44 0.00 35.40 5.19
3363 3518 6.364976 GTGCAAAATTTTAGGTTAATGCGTCT 59.635 34.615 2.44 0.00 35.40 4.18
3366 3521 7.275560 GCAAAATTTTAGGTTAATGCGTCTGAT 59.724 33.333 2.44 0.00 0.00 2.90
3367 3522 9.781834 CAAAATTTTAGGTTAATGCGTCTGATA 57.218 29.630 2.44 0.00 0.00 2.15
3371 3526 6.539649 TTAGGTTAATGCGTCTGATATTGC 57.460 37.500 0.00 0.00 0.00 3.56
3447 3628 6.311200 CCTTTTTGTTCAGAACAGGAAAACAG 59.689 38.462 15.61 9.60 43.27 3.16
3449 3630 6.582677 TTTGTTCAGAACAGGAAAACAGAA 57.417 33.333 15.61 2.05 43.27 3.02
3451 3632 4.096382 TGTTCAGAACAGGAAAACAGAAGC 59.904 41.667 12.24 0.00 36.25 3.86
3452 3633 3.214328 TCAGAACAGGAAAACAGAAGCC 58.786 45.455 0.00 0.00 0.00 4.35
3455 3636 2.568623 ACAGGAAAACAGAAGCCGAT 57.431 45.000 0.00 0.00 0.00 4.18
3475 3659 5.105752 CGATAACTTCTGAAACTCTGGAGG 58.894 45.833 2.58 0.00 0.00 4.30
3482 3666 3.152341 CTGAAACTCTGGAGGTGCATTT 58.848 45.455 0.00 0.00 32.12 2.32
3496 3680 4.757149 AGGTGCATTTGTCTCTGTAAACTC 59.243 41.667 0.00 0.00 0.00 3.01
3527 3713 6.660949 AGATAAGAAACAGAGAAAATGGGTGG 59.339 38.462 0.00 0.00 0.00 4.61
3577 3763 4.562143 GGCCATCTGCAATTGAAAGTCTTT 60.562 41.667 10.34 0.00 43.89 2.52
3692 3878 5.762045 ACAGTTGTATGAATGTGCAAGTTC 58.238 37.500 0.00 0.00 0.00 3.01
3701 3887 2.039818 TGTGCAAGTTCGTGGGTTTA 57.960 45.000 0.00 0.00 0.00 2.01
3708 3894 1.414919 AGTTCGTGGGTTTACTGCAGA 59.585 47.619 23.35 0.48 0.00 4.26
3709 3895 1.529865 GTTCGTGGGTTTACTGCAGAC 59.470 52.381 23.35 8.24 0.00 3.51
3710 3896 0.753867 TCGTGGGTTTACTGCAGACA 59.246 50.000 23.35 4.48 0.00 3.41
3711 3897 1.346395 TCGTGGGTTTACTGCAGACAT 59.654 47.619 23.35 0.00 0.00 3.06
3712 3898 1.464608 CGTGGGTTTACTGCAGACATG 59.535 52.381 23.35 10.29 0.00 3.21
3713 3899 2.504367 GTGGGTTTACTGCAGACATGT 58.496 47.619 23.35 0.00 0.00 3.21
3714 3900 2.226437 GTGGGTTTACTGCAGACATGTG 59.774 50.000 23.35 0.00 0.00 3.21
3715 3901 2.158682 TGGGTTTACTGCAGACATGTGT 60.159 45.455 23.35 0.00 0.00 3.72
3716 3902 2.884639 GGGTTTACTGCAGACATGTGTT 59.115 45.455 23.35 0.00 0.00 3.32
3717 3903 3.317993 GGGTTTACTGCAGACATGTGTTT 59.682 43.478 23.35 0.00 0.00 2.83
3718 3904 4.290155 GGTTTACTGCAGACATGTGTTTG 58.710 43.478 23.35 0.00 33.75 2.93
3719 3905 4.202010 GGTTTACTGCAGACATGTGTTTGT 60.202 41.667 23.35 0.12 33.24 2.83
3720 3906 4.550577 TTACTGCAGACATGTGTTTGTG 57.449 40.909 23.35 0.00 33.24 3.33
3721 3907 2.642427 ACTGCAGACATGTGTTTGTGA 58.358 42.857 23.35 0.00 33.24 3.58
3722 3908 2.615447 ACTGCAGACATGTGTTTGTGAG 59.385 45.455 23.35 2.75 33.24 3.51
3723 3909 2.615447 CTGCAGACATGTGTTTGTGAGT 59.385 45.455 8.42 0.00 33.24 3.41
3724 3910 3.016031 TGCAGACATGTGTTTGTGAGTT 58.984 40.909 1.15 0.00 33.24 3.01
3725 3911 3.443329 TGCAGACATGTGTTTGTGAGTTT 59.557 39.130 1.15 0.00 33.24 2.66
3726 3912 4.637977 TGCAGACATGTGTTTGTGAGTTTA 59.362 37.500 1.15 0.00 33.24 2.01
3727 3913 5.124617 TGCAGACATGTGTTTGTGAGTTTAA 59.875 36.000 1.15 0.00 33.24 1.52
3728 3914 5.682862 GCAGACATGTGTTTGTGAGTTTAAG 59.317 40.000 1.15 0.00 33.24 1.85
3729 3915 6.677920 GCAGACATGTGTTTGTGAGTTTAAGT 60.678 38.462 1.15 0.00 33.24 2.24
3730 3916 6.907212 CAGACATGTGTTTGTGAGTTTAAGTC 59.093 38.462 1.15 0.00 0.00 3.01
3731 3917 6.823689 AGACATGTGTTTGTGAGTTTAAGTCT 59.176 34.615 1.15 0.00 0.00 3.24
3732 3918 7.985184 AGACATGTGTTTGTGAGTTTAAGTCTA 59.015 33.333 1.15 0.00 0.00 2.59
3733 3919 8.677148 ACATGTGTTTGTGAGTTTAAGTCTAT 57.323 30.769 0.00 0.00 0.00 1.98
3734 3920 9.120538 ACATGTGTTTGTGAGTTTAAGTCTATT 57.879 29.630 0.00 0.00 0.00 1.73
3735 3921 9.950680 CATGTGTTTGTGAGTTTAAGTCTATTT 57.049 29.630 1.30 0.00 0.00 1.40
3749 3935 6.976636 AAGTCTATTTTTAGAGAGCTGTGC 57.023 37.500 0.00 0.00 0.00 4.57
3750 3936 6.293004 AGTCTATTTTTAGAGAGCTGTGCT 57.707 37.500 0.00 0.00 43.88 4.40
3751 3937 7.411486 AGTCTATTTTTAGAGAGCTGTGCTA 57.589 36.000 0.00 0.00 39.88 3.49
3752 3938 7.488322 AGTCTATTTTTAGAGAGCTGTGCTAG 58.512 38.462 0.00 0.00 39.88 3.42
3753 3939 7.340743 AGTCTATTTTTAGAGAGCTGTGCTAGA 59.659 37.037 0.00 0.00 39.88 2.43
3754 3940 7.434013 GTCTATTTTTAGAGAGCTGTGCTAGAC 59.566 40.741 0.00 0.00 39.88 2.59
3755 3941 3.766676 TTTAGAGAGCTGTGCTAGACG 57.233 47.619 0.00 0.00 39.88 4.18
3756 3942 1.018148 TAGAGAGCTGTGCTAGACGC 58.982 55.000 0.00 0.00 39.88 5.19
3799 3985 8.052490 CACATATGAATACTCAATATAAGCGCG 58.948 37.037 10.38 0.00 34.49 6.86
3801 3987 5.822584 TGAATACTCAATATAAGCGCGTG 57.177 39.130 8.43 0.00 0.00 5.34
3812 4001 0.866061 AAGCGCGTGTATGCTAGACG 60.866 55.000 8.43 8.00 46.70 4.18
3813 4002 1.585521 GCGCGTGTATGCTAGACGT 60.586 57.895 8.43 0.00 45.84 4.34
3814 4003 2.195615 CGCGTGTATGCTAGACGTG 58.804 57.895 0.00 11.22 46.59 4.49
3909 4098 4.984161 CACTTGGTATGGCAAAGAAAGTTG 59.016 41.667 3.78 0.00 32.43 3.16
3911 4100 2.896685 TGGTATGGCAAAGAAAGTTGGG 59.103 45.455 0.00 0.00 0.00 4.12
3932 4122 1.868713 TGCATTCCATCAAGCCCAAT 58.131 45.000 0.00 0.00 0.00 3.16
3960 4150 4.165758 AGGATTCCAGGTCGTAGTAGTACT 59.834 45.833 8.14 8.14 0.00 2.73
3961 4151 4.275443 GGATTCCAGGTCGTAGTAGTACTG 59.725 50.000 13.29 0.00 0.00 2.74
4032 4222 9.849166 TTTAGTTTTACAACAAAAGGACTTGAG 57.151 29.630 0.00 0.00 35.05 3.02
4138 4337 3.482436 TGCACTTACCGAGTTTCCATTT 58.518 40.909 0.00 0.00 36.10 2.32
4148 4347 3.149196 GAGTTTCCATTTGCTCCTGTCA 58.851 45.455 0.00 0.00 0.00 3.58
4152 4351 2.439409 TCCATTTGCTCCTGTCACATG 58.561 47.619 0.00 0.00 0.00 3.21
4233 4432 9.971922 GAATAATTTCACAGAAAGATTATGGGG 57.028 33.333 0.00 0.00 0.00 4.96
4234 4433 9.713684 AATAATTTCACAGAAAGATTATGGGGA 57.286 29.630 0.00 0.00 0.00 4.81
4235 4434 9.887862 ATAATTTCACAGAAAGATTATGGGGAT 57.112 29.630 0.00 0.00 0.00 3.85
4236 4435 8.613922 AATTTCACAGAAAGATTATGGGGATT 57.386 30.769 0.00 0.00 0.00 3.01
4237 4436 8.613922 ATTTCACAGAAAGATTATGGGGATTT 57.386 30.769 0.00 0.00 0.00 2.17
4238 4437 9.713684 ATTTCACAGAAAGATTATGGGGATTTA 57.286 29.630 0.00 0.00 0.00 1.40
4239 4438 8.519799 TTCACAGAAAGATTATGGGGATTTAC 57.480 34.615 0.00 0.00 0.00 2.01
4240 4439 7.872138 TCACAGAAAGATTATGGGGATTTACT 58.128 34.615 0.00 0.00 0.00 2.24
4241 4440 8.336235 TCACAGAAAGATTATGGGGATTTACTT 58.664 33.333 0.00 0.00 0.00 2.24
4242 4441 8.971073 CACAGAAAGATTATGGGGATTTACTTT 58.029 33.333 0.00 0.00 0.00 2.66
4243 4442 9.547279 ACAGAAAGATTATGGGGATTTACTTTT 57.453 29.630 0.00 0.00 0.00 2.27
4245 4444 9.768215 AGAAAGATTATGGGGATTTACTTTTCA 57.232 29.630 0.00 0.00 0.00 2.69
4248 4447 9.713684 AAGATTATGGGGATTTACTTTTCATGA 57.286 29.630 0.00 0.00 0.00 3.07
4249 4448 9.136323 AGATTATGGGGATTTACTTTTCATGAC 57.864 33.333 0.00 0.00 0.00 3.06
4250 4449 5.835113 ATGGGGATTTACTTTTCATGACG 57.165 39.130 0.00 0.00 0.00 4.35
4251 4450 3.442273 TGGGGATTTACTTTTCATGACGC 59.558 43.478 0.00 0.00 0.00 5.19
4252 4451 3.694566 GGGGATTTACTTTTCATGACGCT 59.305 43.478 0.00 0.00 0.00 5.07
4253 4452 4.157840 GGGGATTTACTTTTCATGACGCTT 59.842 41.667 0.00 0.00 0.00 4.68
4254 4453 5.336451 GGGGATTTACTTTTCATGACGCTTT 60.336 40.000 0.00 0.00 0.00 3.51
4255 4454 5.572896 GGGATTTACTTTTCATGACGCTTTG 59.427 40.000 0.00 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.321564 GACACCTGTGGCAGCATGTA 60.322 55.000 0.00 0.00 38.82 2.29
1 2 1.601759 GACACCTGTGGCAGCATGT 60.602 57.895 0.00 4.63 38.82 3.21
2 3 0.892358 AAGACACCTGTGGCAGCATG 60.892 55.000 5.83 0.00 42.32 4.06
3 4 0.607489 GAAGACACCTGTGGCAGCAT 60.607 55.000 5.83 0.00 42.32 3.79
4 5 1.227943 GAAGACACCTGTGGCAGCA 60.228 57.895 5.83 0.00 42.32 4.41
5 6 1.072159 AGAAGACACCTGTGGCAGC 59.928 57.895 5.83 0.00 42.32 5.25
6 7 0.604780 CCAGAAGACACCTGTGGCAG 60.605 60.000 5.83 0.00 42.32 4.85
7 8 1.451504 CCAGAAGACACCTGTGGCA 59.548 57.895 5.83 0.00 42.32 4.92
8 9 1.968540 GCCAGAAGACACCTGTGGC 60.969 63.158 1.91 0.00 42.59 5.01
9 10 0.179020 TTGCCAGAAGACACCTGTGG 60.179 55.000 1.91 0.00 32.85 4.17
10 11 1.233019 CTTGCCAGAAGACACCTGTG 58.767 55.000 0.00 0.00 0.00 3.66
11 12 0.109342 CCTTGCCAGAAGACACCTGT 59.891 55.000 0.00 0.00 0.00 4.00
12 13 0.109342 ACCTTGCCAGAAGACACCTG 59.891 55.000 0.00 0.00 0.00 4.00
13 14 0.109342 CACCTTGCCAGAAGACACCT 59.891 55.000 0.00 0.00 0.00 4.00
14 15 0.108585 TCACCTTGCCAGAAGACACC 59.891 55.000 0.00 0.00 0.00 4.16
15 16 1.808945 CATCACCTTGCCAGAAGACAC 59.191 52.381 0.00 0.00 0.00 3.67
16 17 1.271543 CCATCACCTTGCCAGAAGACA 60.272 52.381 0.00 0.00 0.00 3.41
39 40 2.125310 TCGCCAATACCGCCACTG 60.125 61.111 0.00 0.00 0.00 3.66
40 41 2.125269 GTCGCCAATACCGCCACT 60.125 61.111 0.00 0.00 0.00 4.00
41 42 3.560278 CGTCGCCAATACCGCCAC 61.560 66.667 0.00 0.00 0.00 5.01
62 63 0.895530 ACCGGATTCTGCTTCTTCGA 59.104 50.000 9.46 0.00 0.00 3.71
64 65 0.729690 GCACCGGATTCTGCTTCTTC 59.270 55.000 9.46 0.00 0.00 2.87
70 71 1.718757 GACATGGCACCGGATTCTGC 61.719 60.000 9.46 7.49 0.00 4.26
129 130 0.328258 TAGTGCTTGGGAAGAAGGCC 59.672 55.000 0.00 0.00 0.00 5.19
132 133 3.703001 TTCCTAGTGCTTGGGAAGAAG 57.297 47.619 3.19 0.00 34.64 2.85
141 142 1.452108 GCGGCCATTCCTAGTGCTT 60.452 57.895 2.24 0.00 0.00 3.91
142 143 2.190578 GCGGCCATTCCTAGTGCT 59.809 61.111 2.24 0.00 0.00 4.40
159 160 1.862602 CTTGGAAAAGGAACCCGCGG 61.863 60.000 21.04 21.04 0.00 6.46
180 181 2.232452 CTGAACCAAGATGAGACGACCT 59.768 50.000 0.00 0.00 0.00 3.85
200 201 0.389948 GATTGCGGAGAACACGGACT 60.390 55.000 0.00 0.00 0.00 3.85
201 202 1.359459 GGATTGCGGAGAACACGGAC 61.359 60.000 0.00 0.00 0.00 4.79
202 203 1.079405 GGATTGCGGAGAACACGGA 60.079 57.895 0.00 0.00 0.00 4.69
203 204 0.673644 AAGGATTGCGGAGAACACGG 60.674 55.000 0.00 0.00 0.00 4.94
204 205 2.004583 TAAGGATTGCGGAGAACACG 57.995 50.000 0.00 0.00 0.00 4.49
205 206 3.798202 AGATAAGGATTGCGGAGAACAC 58.202 45.455 0.00 0.00 0.00 3.32
206 207 4.191544 CAAGATAAGGATTGCGGAGAACA 58.808 43.478 0.00 0.00 0.00 3.18
207 208 4.034510 CACAAGATAAGGATTGCGGAGAAC 59.965 45.833 0.00 0.00 0.00 3.01
208 209 4.191544 CACAAGATAAGGATTGCGGAGAA 58.808 43.478 0.00 0.00 0.00 2.87
209 210 3.197766 ACACAAGATAAGGATTGCGGAGA 59.802 43.478 0.00 0.00 0.00 3.71
210 211 3.535561 ACACAAGATAAGGATTGCGGAG 58.464 45.455 0.00 0.00 0.00 4.63
211 212 3.627395 ACACAAGATAAGGATTGCGGA 57.373 42.857 0.00 0.00 0.00 5.54
212 213 4.396166 AGAAACACAAGATAAGGATTGCGG 59.604 41.667 0.00 0.00 0.00 5.69
213 214 5.327091 CAGAAACACAAGATAAGGATTGCG 58.673 41.667 0.00 0.00 0.00 4.85
214 215 5.098211 GCAGAAACACAAGATAAGGATTGC 58.902 41.667 0.00 0.00 0.00 3.56
215 216 5.416952 AGGCAGAAACACAAGATAAGGATTG 59.583 40.000 0.00 0.00 0.00 2.67
249 250 4.387256 GGTGCTCAGCGAATCAGATTATAC 59.613 45.833 0.00 0.00 0.00 1.47
278 279 1.303317 GGCGTTCCAGTGGACCAAT 60.303 57.895 12.69 0.00 0.00 3.16
301 302 2.040544 GGGTGCATGGAACGTCTGG 61.041 63.158 0.00 0.00 0.00 3.86
307 308 2.040544 CCGAGTGGGTGCATGGAAC 61.041 63.158 0.00 0.00 0.00 3.62
324 325 2.859165 TGGGAGAAATGACACTGACC 57.141 50.000 0.00 0.00 0.00 4.02
382 384 7.228706 GGTTGAACGGGTCATTTCTATCAATAT 59.771 37.037 0.00 0.00 35.70 1.28
384 386 5.357032 GGTTGAACGGGTCATTTCTATCAAT 59.643 40.000 0.00 0.00 35.70 2.57
458 482 5.468072 GTGCTATATGTCAACAGATCCTTGG 59.532 44.000 0.00 0.00 0.00 3.61
495 519 5.478233 ACGTGCTATATTCGATGCAAAAA 57.522 34.783 0.00 0.00 37.17 1.94
497 521 5.286438 AGTACGTGCTATATTCGATGCAAA 58.714 37.500 3.62 0.00 37.17 3.68
498 522 4.866921 AGTACGTGCTATATTCGATGCAA 58.133 39.130 3.62 0.00 37.17 4.08
499 523 4.023536 TGAGTACGTGCTATATTCGATGCA 60.024 41.667 6.01 0.00 0.00 3.96
500 524 4.473199 TGAGTACGTGCTATATTCGATGC 58.527 43.478 6.01 0.00 0.00 3.91
501 525 7.568267 AAATGAGTACGTGCTATATTCGATG 57.432 36.000 6.01 0.00 0.00 3.84
502 526 9.290483 CATAAATGAGTACGTGCTATATTCGAT 57.710 33.333 6.01 5.64 0.00 3.59
503 527 8.508875 TCATAAATGAGTACGTGCTATATTCGA 58.491 33.333 6.01 6.09 32.11 3.71
504 528 8.669394 TCATAAATGAGTACGTGCTATATTCG 57.331 34.615 6.01 4.10 32.11 3.34
656 726 7.473511 CGGAATAGGGATATGGGGAAAGATATC 60.474 44.444 0.00 0.00 32.77 1.63
839 911 7.489574 TTATACAGCACGAATGATTAATGCA 57.510 32.000 13.58 0.00 38.79 3.96
903 976 7.489574 TTATACAGCACGAATGATTAATGCA 57.510 32.000 13.58 0.00 38.79 3.96
937 1012 3.732212 TGCTGGAATAGGATCAATCACG 58.268 45.455 0.00 0.00 0.00 4.35
1068 1152 4.394300 GTGGCATCTGGATTGATATAGCAC 59.606 45.833 0.00 0.00 0.00 4.40
1128 1212 1.742900 CGAGCACGATGTAAGCACGG 61.743 60.000 0.00 0.00 42.66 4.94
1389 1473 1.134491 CCGTTCTTTAGCCCGAGGAAT 60.134 52.381 0.00 0.00 0.00 3.01
1484 1568 0.250338 GTCGTCAAAGGAAGGGTGCT 60.250 55.000 0.00 0.00 0.00 4.40
1629 1713 3.036084 GTGGACGAGGTGTGCGTG 61.036 66.667 0.00 0.00 42.78 5.34
1739 1827 0.307760 GGCGCATACCTTGTACATGC 59.692 55.000 10.83 8.09 41.29 4.06
1954 2049 1.153369 CGTTGGTGATCGAGCCCAT 60.153 57.895 10.95 0.00 0.00 4.00
2051 2146 1.590259 GCTTCTCCGTCGATGCTCC 60.590 63.158 0.00 0.00 32.95 4.70
2090 2185 2.771943 AGAGGGTGTGACTTTGAACTCA 59.228 45.455 0.00 0.00 0.00 3.41
2134 2229 5.008019 CACTGTCACTCTTGTAATTGCAGTT 59.992 40.000 0.00 0.00 33.13 3.16
2436 2534 1.817740 CGGGAAGAGAAAAAGGGCACA 60.818 52.381 0.00 0.00 0.00 4.57
2619 2718 5.591877 GTCAGGATGGATGCTTTTGATAAGT 59.408 40.000 0.00 0.00 36.16 2.24
2850 2949 3.775654 GCTAGGCCGCTGTCACCT 61.776 66.667 0.00 0.00 37.61 4.00
2979 3078 0.655733 CGTTTGTCACAGTCCGCTTT 59.344 50.000 0.00 0.00 0.00 3.51
3024 3123 4.681978 GGCGCGTCCACCTTCACT 62.682 66.667 8.43 0.00 34.01 3.41
3207 3306 0.397941 CTCTTGGGGAGACAGCAACA 59.602 55.000 0.00 0.00 44.45 3.33
3240 3339 3.828921 CATCATTCATGGTGATGGGTCT 58.171 45.455 23.34 1.36 45.75 3.85
3356 3511 3.371102 AGTACGCAATATCAGACGCAT 57.629 42.857 0.00 0.00 0.00 4.73
3357 3512 2.857748 CAAGTACGCAATATCAGACGCA 59.142 45.455 0.00 0.00 0.00 5.24
3358 3513 3.113322 TCAAGTACGCAATATCAGACGC 58.887 45.455 0.00 0.00 0.00 5.19
3360 3515 7.230222 GCAATATCAAGTACGCAATATCAGAC 58.770 38.462 0.00 0.00 0.00 3.51
3362 3517 6.128822 ACGCAATATCAAGTACGCAATATCAG 60.129 38.462 0.00 0.00 0.00 2.90
3363 3518 5.694458 ACGCAATATCAAGTACGCAATATCA 59.306 36.000 0.00 0.00 0.00 2.15
3366 3521 4.446385 GGACGCAATATCAAGTACGCAATA 59.554 41.667 0.00 0.00 0.00 1.90
3367 3522 3.247648 GGACGCAATATCAAGTACGCAAT 59.752 43.478 0.00 0.00 0.00 3.56
3369 3524 2.159156 AGGACGCAATATCAAGTACGCA 60.159 45.455 0.00 0.00 0.00 5.24
3371 3526 2.218759 GCAGGACGCAATATCAAGTACG 59.781 50.000 0.00 0.00 41.79 3.67
3447 3628 5.062809 CAGAGTTTCAGAAGTTATCGGCTTC 59.937 44.000 0.00 0.00 41.78 3.86
3449 3630 4.499183 CAGAGTTTCAGAAGTTATCGGCT 58.501 43.478 0.00 0.00 0.00 5.52
3451 3632 5.073311 TCCAGAGTTTCAGAAGTTATCGG 57.927 43.478 0.00 0.00 0.00 4.18
3452 3633 5.105752 CCTCCAGAGTTTCAGAAGTTATCG 58.894 45.833 0.00 0.00 0.00 2.92
3455 3636 4.503296 GCACCTCCAGAGTTTCAGAAGTTA 60.503 45.833 0.00 0.00 0.00 2.24
3475 3659 5.931441 AGAGTTTACAGAGACAAATGCAC 57.069 39.130 0.00 0.00 0.00 4.57
3482 3666 6.656632 ATCTGACAAGAGTTTACAGAGACA 57.343 37.500 0.00 0.00 40.17 3.41
3496 3680 9.823098 CATTTTCTCTGTTTCTTATCTGACAAG 57.177 33.333 0.00 0.00 0.00 3.16
3527 3713 2.003301 GGACACAATCGCCTCTCTTTC 58.997 52.381 0.00 0.00 0.00 2.62
3577 3763 2.301583 GGGGGTCTGCATTAAAGCAAAA 59.698 45.455 6.84 0.00 45.13 2.44
3580 3766 3.281332 GGGGGTCTGCATTAAAGCA 57.719 52.632 5.13 5.13 43.35 3.91
3692 3878 1.464608 CATGTCTGCAGTAAACCCACG 59.535 52.381 14.67 0.00 0.00 4.94
3701 3887 2.615447 CTCACAAACACATGTCTGCAGT 59.385 45.455 14.67 0.00 0.00 4.40
3708 3894 8.677148 ATAGACTTAAACTCACAAACACATGT 57.323 30.769 0.00 0.00 0.00 3.21
3709 3895 9.950680 AAATAGACTTAAACTCACAAACACATG 57.049 29.630 0.00 0.00 0.00 3.21
3723 3909 8.936864 GCACAGCTCTCTAAAAATAGACTTAAA 58.063 33.333 0.00 0.00 0.00 1.52
3724 3910 8.314751 AGCACAGCTCTCTAAAAATAGACTTAA 58.685 33.333 0.00 0.00 30.62 1.85
3725 3911 7.841956 AGCACAGCTCTCTAAAAATAGACTTA 58.158 34.615 0.00 0.00 30.62 2.24
3726 3912 6.706295 AGCACAGCTCTCTAAAAATAGACTT 58.294 36.000 0.00 0.00 30.62 3.01
3727 3913 6.293004 AGCACAGCTCTCTAAAAATAGACT 57.707 37.500 0.00 0.00 30.62 3.24
3728 3914 7.434013 GTCTAGCACAGCTCTCTAAAAATAGAC 59.566 40.741 0.00 0.00 40.44 2.59
3729 3915 7.484975 GTCTAGCACAGCTCTCTAAAAATAGA 58.515 38.462 0.00 0.00 40.44 1.98
3730 3916 6.416455 CGTCTAGCACAGCTCTCTAAAAATAG 59.584 42.308 0.00 0.00 40.44 1.73
3731 3917 6.266323 CGTCTAGCACAGCTCTCTAAAAATA 58.734 40.000 0.00 0.00 40.44 1.40
3732 3918 5.105752 CGTCTAGCACAGCTCTCTAAAAAT 58.894 41.667 0.00 0.00 40.44 1.82
3733 3919 4.486090 CGTCTAGCACAGCTCTCTAAAAA 58.514 43.478 0.00 0.00 40.44 1.94
3734 3920 4.098055 CGTCTAGCACAGCTCTCTAAAA 57.902 45.455 0.00 0.00 40.44 1.52
3735 3921 3.766676 CGTCTAGCACAGCTCTCTAAA 57.233 47.619 0.00 0.00 40.44 1.85
3748 3934 2.544267 ACAAAGACAACTTGCGTCTAGC 59.456 45.455 0.00 0.00 42.90 3.42
3749 3935 4.795970 AACAAAGACAACTTGCGTCTAG 57.204 40.909 0.00 0.00 42.90 2.43
3750 3936 5.122554 TGAAAACAAAGACAACTTGCGTCTA 59.877 36.000 0.00 0.00 42.90 2.59
3751 3937 4.083003 TGAAAACAAAGACAACTTGCGTCT 60.083 37.500 0.00 0.00 45.62 4.18
3752 3938 4.030195 GTGAAAACAAAGACAACTTGCGTC 59.970 41.667 0.00 0.00 36.39 5.19
3753 3939 3.917985 GTGAAAACAAAGACAACTTGCGT 59.082 39.130 0.00 0.00 36.39 5.24
3754 3940 3.917380 TGTGAAAACAAAGACAACTTGCG 59.083 39.130 0.00 0.00 36.39 4.85
3755 3941 7.434897 TCATATGTGAAAACAAAGACAACTTGC 59.565 33.333 1.90 0.00 36.39 4.01
3756 3942 8.854979 TCATATGTGAAAACAAAGACAACTTG 57.145 30.769 1.90 0.00 36.39 3.16
3772 3958 9.087424 GCGCTTATATTGAGTATTCATATGTGA 57.913 33.333 0.00 0.00 32.27 3.58
3773 3959 8.052490 CGCGCTTATATTGAGTATTCATATGTG 58.948 37.037 5.56 0.00 32.27 3.21
3795 3981 1.585521 ACGTCTAGCATACACGCGC 60.586 57.895 5.73 0.00 37.02 6.86
3797 3983 1.904144 TTCACGTCTAGCATACACGC 58.096 50.000 1.20 0.00 37.02 5.34
3799 3985 6.036083 ACATGAATTTCACGTCTAGCATACAC 59.964 38.462 0.00 0.00 0.00 2.90
3801 3987 6.589830 ACATGAATTTCACGTCTAGCATAC 57.410 37.500 0.00 0.00 0.00 2.39
3813 4002 9.979578 ACAAAAGCACTATAAACATGAATTTCA 57.020 25.926 0.00 0.75 0.00 2.69
3840 4029 1.872952 TGCGCTTATATCACACATGGC 59.127 47.619 9.73 0.00 0.00 4.40
3911 4100 1.405872 TGGGCTTGATGGAATGCATC 58.594 50.000 7.84 7.84 0.00 3.91
3932 4122 2.471815 ACGACCTGGAATCCTGGATA 57.528 50.000 28.69 0.00 44.09 2.59
3960 4150 4.159321 TGAAAGACCAAACAAGAATGCACA 59.841 37.500 0.00 0.00 0.00 4.57
3961 4151 4.504097 GTGAAAGACCAAACAAGAATGCAC 59.496 41.667 0.00 0.00 0.00 4.57
4032 4222 6.122964 AGGAAGGAGATTAAGGTAACAATGC 58.877 40.000 0.00 0.00 41.41 3.56
4138 4337 0.770499 TTTCCCATGTGACAGGAGCA 59.230 50.000 0.00 0.00 0.00 4.26
4148 4347 3.647590 AGCCAAAGAAACATTTCCCATGT 59.352 39.130 0.68 0.00 37.92 3.21
4152 4351 6.405842 CCATAGTAGCCAAAGAAACATTTCCC 60.406 42.308 0.68 0.00 37.92 3.97


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.